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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2012	Nov. 02, 2012
Document and Entity Information
Entity Registrant Name	METABOLIX, INC.
Entity Central Index Key	0001121702
Document Type	10-Q
Document Period End Date	Sep. 30, 2012
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		34,306,570
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	Q3

CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Sep. 30, 2012	Dec. 31, 2011
Current Assets:
Cash and cash equivalents	$ 17,405	$ 21,277
Short-term investments	30,418	55,578
Accounts receivable	654	146
Due from related parties		311
Unbilled receivables	667	304
Prepaid expenses and other current assets	707	823
Inventory	3,028
Total current assets	52,879	78,439
Restricted cash	594	622
Property and equipment, net	1,634	2,276
Long-term investments	5,767	1,503
Other assets	95	72
Total assets	60,969	82,912
Current Liabilities:
Accounts payable	240	512
Accrued expenses	3,488	3,574
Current portion of deferred rent	165	165
Short-term deferred revenue	959	2,914
Total current liabilities	4,852	7,165
Deferred rent, net of current portion	97	221
Long-term deferred revenue		35,944
Other long-term liabilities	128	119
Total liabilities	5,077	43,449
Commitments and contingencies (Note 12)
Stockholders' Equity:
Preferred stock ($0.01 par value per share); 5,000,000 shares authorized; no shares issued or outstanding
Common stock ($0.01 par value per share); 100,000,000 shares authorized at September 30, 2012 and December 31, 2011, 34,250,180 and 34,115,798 shares issued and outstanding at September 30, 2012 and December 31, 2011, respectively	343	341
Additional paid-in capital	288,084	284,796
Accumulated other comprehensive loss	(20)	(12)
Accumulated deficit	(232,515)	(245,662)
Total stockholders' equity	55,892	39,463
Total liabilities and stockholders' equity	$ 60,969	$ 82,912

CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares	Sep. 30, 2012	Dec. 31, 2011
CONSOLIDATED BALANCE SHEETS
Preferred stock, par value per share (in dollars per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value per share (in dollars per share)	$ 0.01	$ 0.01
Common stock, shares authorized	100,000,000	100,000,000
Common stock, shares issued	34,250,180	34,115,798
Common stock, shares outstanding	34,250,180	34,115,798

CONSOLIDATED STATEMENTS OF OPERATIONS - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Revenue:
Revenue from termination of ADM collaboration			$ 38,885
Grant revenue	$ 576	$ 443	1,415	$ 567
License fee and royalty revenue from related parties	28	26	162	419
Product revenue	70		457
Total revenue	674	469	40,919	986
Costs and expenses:
Cost of product revenue	316		808
Research and development	4,931	6,153	15,982	18,352
Selling, general, and administrative	3,170	3,895	11,006	11,878
Total costs and expenses	8,417	10,048	27,796	30,230
Income (loss) from operations	(7,743)	(9,579)	13,123	(29,244)
Other income (expense):
Interest income, net	(2)	19	24	62
Net income (loss)	$ (7,745)	$ (9,560)	$ 13,147	$ (29,182)
Net income (loss) per share:
Basic (in dollars per share)	$ (0.23)	$ (0.28)	$ 0.38	$ (0.96)
Diluted (in dollars per share)	$ (0.23)	$ (0.28)	$ 0.38	$ (0.96)
Number of shares used in per share calculations:
Basic (in shares)	34,243,792	34,080,177	34,188,146	30,295,881
Diluted (in shares)	34,243,792	34,080,177	34,270,455	30,295,881

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Net income (loss):	$ (7,745)	$ (9,560)	$ 13,147	$ (29,182)
Other comprehensive income (loss)
Change in unrealized gain (loss) on investments	12	7	(6)	(1)
Change in foreign currency translation adjustment	3	(12)	(2)	(16)
Total other comprehensive income (loss)	15	(5)	(8)	(17)
Comprehensive income (loss)	$ (7,730)	$ (9,565)	$ 13,139	$ (29,199)

- Definition

The change in equity [net assets] of a business enterprise during a period from transactions and other events and circumstances from non-owner sources which are attributable to the reporting entity. It includes all changes in equity during a period except those resulting from investments by owners and distributions to owners, but excludes any and all transactions which are directly or indirectly attributable to that ownership interest in subsidiary equity which is not attributable to the parent.

+ References + Details

- Definition

Amount after tax and reclassification adjustments, resulting from the process of expressing in the reporting currency of the reporting entity those amounts that are denominated or measured in a different currency, and from transactions whose terms are denominated in a currency other than the entity's functional currency, which is attributable to the parent entity.

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- Definition

Net of tax amount of other comprehensive income (loss) attributable to the parent entity.

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- Definition

Net of tax amount of unrealized holding gain (loss) before reclassification adjustments and transfers on available-for-sale securities.

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+ Details

CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Cash flows from operating activities
Net income (loss)	$ 13,147	$ (29,182)
Adjustments to reconcile net income (loss) to cash used in operating activities:
Depreciation	1,026	1,134
Charge for 401(k) company common stock match	350	489
Stock-based compensation	2,935	3,574
Changes in operating assets and liabilities:
Receivables (billed and unbilled)	(871)	(448)
Due from related party	311	(88)
Prepaid expenses and other assets	94	429
Inventory	(3,028)
Accounts payable	(272)	289
Accrued expenses	(101)	(541)
Deferred rent and other long-term liabilities	(115)	(115)
Deferred revenue	(37,900)	1,335
Net cash used in operating activities	(24,424)	(23,124)
Cash flows from investing activities
Purchase of property and equipment	(397)	(627)
Proceeds from sale of property and equipment	12
Change in restricted cash	28
Purchase of investments	(56,428)	(93,888)
Proceeds from the sale and maturity of short-term investments	77,320	73,112
Net cash provided by (used in) investing activities	20,535	(21,403)
Cash flows from financing activities
Proceeds from options exercised	19	71
Proceeds from public stock offering, net of offering costs of $2,360		49,333
Net cash provided by financing activities	19	49,404
Effect of exchange rate changes on cash and cash equivalents	(2)	(11)
Net (decrease) increase in cash and cash equivalents	(3,872)	4,866
Cash and cash equivalents at beginning of period	21,277	12,526
Cash and cash equivalents at end of period	$ 17,405	$ 17,392

CONSOLIDATED STATEMENTS OF CASH FLOWS (Parenthetical) $ in Thousands	9 Months Ended
	Sep. 30, 2011 USD ($)
CONSOLIDATED STATEMENTS OF CASH FLOWS
Proceeds from public stock offering, offering costs	$ 2,360

BASIS OF PRESENTATION

9 Months Ended

Sep. 30, 2012

BASIS OF PRESENTATION

BASIS OF PRESENTATION

1. BASIS OF PRESENTATION

The accompanying consolidated financial statements are unaudited and have been prepared by Metabolix, Inc. (the “Company”) in accordance with accounting principles generally accepted in the United States of America (“GAAP”) and pursuant to the rules and regulations of the U.S. Securities and Exchange Commission (“SEC”). Certain information and footnote disclosures normally included in the Company’s annual consolidated financial statements have been condensed or omitted. The year-end consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The consolidated financial statements, in the opinion of management, reflect all adjustments (consisting only of normal recurring adjustments) necessary for a fair statement of the financial position and results of operations for the interim periods ended September 30, 2012 and 2011.

The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for any future period or the entire fiscal year. These interim consolidated financial statements should be read in conjunction with the audited consolidated financial statements for the year ended December 31, 2011, which are contained in the Company’s Annual Report on Form 10-K filed with the SEC on March 12, 2012.

ACCOUNTING POLICIES

9 Months Ended

Sep. 30, 2012

ACCOUNTING POLICIES

ACCOUNTING POLICIES

2. ACCOUNTING POLICIES

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates.

Inventory

During March 2012, the Company acquired raw material and finished goods inventory of biopolymer from Telles, LLC as described in Note 16. The Company’s adopted inventory policies as a result of this transaction are to state inventory at the lower of cost or market and to value inventory using the average cost method. The Company analyzes its inventory levels quarterly and writes down, to cost of product revenue, inventory that has become obsolete, inventory in excess of expected sales requirements or inventory that fails to meet commercial sales specifications.

Revenue Recognition

During March 2012, the Company initiated biopolymer product sales to customers for the first time. The Company’s policy is to recognize revenue when evidence of an arrangement exists, title has passed or services have been rendered, the selling price is fixed or determinable and collectability is reasonably assured. Revenue from product sales to customers is recognized when all elements of the sale have been delivered. All costs related to product shipment are recognized at time of shipment. During the Company’s six months ended June 30, 2012, it did not provide for rights of return to customers on product sales, except for situations where the product did not meet the technical specifications. The Company modified its product return policy prospectively during its fiscal quarter ending September 30, 2012 to allow discretion in accepting returns during a period of sixty days after product delivery. Until sufficient experience is developed on which to base an estimate of returns, the Company defers recognition of product revenue until the sixty day period has elapsed.

The Company recognizes funds received from contractual research and development services and from government grants as revenue. These contracts and grants are considered an ongoing major and central operation of the Company’s business. For government grants, revenue is earned as research expenses related to the grants are incurred.

There has been no other material change in accounting policies since the Company’s fiscal year ended December 31, 2011, as described in Note 2 to the consolidated financial statements included in its Annual Report on Form 10-K for the year then ended.

RECENT ACCOUNTING PRONOUNCEMENTS

9 Months Ended

Sep. 30, 2012

RECENT ACCOUNTING PRONOUNCEMENTS

RECENT ACCOUNTING PRONOUNCEMENTS

3. RECENT ACCOUNTING PRONOUNCEMENTS

In June 2011, the Financial Accounting Standards Board (“FASB”) issued an accounting standards update that eliminates the option to present components of other comprehensive income as part of the statement of changes in equity and requires an entity to present items of net income and other comprehensive income either in a single continuous statement of comprehensive income or in two separate but consecutive statements. This guidance also requires an entity to present on the face of the financial statements reclassification adjustments from other comprehensive income to net income. This guidance became effective for fiscal years beginning after December 15, 2011. In December 2011, the FASB issued an accounting standards update that defers the presentation requirement for other comprehensive income reclassifications on the face of the financial statements. The Company adopted the provisions of the guidance in its first quarter of 2012 and elected to present items of net income and other comprehensive income in two separate but consecutive statements.

- Definition

The entire disclosure of changes in accounting principles, including adoption of new accounting pronouncements, that describes the new methods, amount and effects on financial statement line items.

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+ Details

BASIC AND DILUTED NET INCOME (LOSS) PER SHARE

9 Months Ended

Sep. 30, 2012

BASIC AND DILUTED NET INCOME (LOSS) PER SHARE

BASIC AND DILUTED NET INCOME (LOSS) PER SHARE

4. BASIC AND DILUTED NET INCOME (LOSS) PER SHARE

Basic net income (loss) per share is computed by dividing net income (loss) by the weighted-average number of common shares outstanding. Common stock equivalents include stock options and warrants. Diluted net income per share is computed by dividing net income by the weighted-average number of dilutive common shares outstanding during the period. Diluted shares outstanding is calculated by adding to the weighted shares outstanding any potential (unissued) shares of common stock from outstanding stock options and warrants based on the treasury stock method. In periods when a net loss is reported, all common stock equivalents are excluded from the calculation because they would have an anti-dilutive effect, meaning the loss per share would be reduced. Therefore, in periods when a loss is reported there is no difference in basic and diluted loss per share.

Shares used to calculate diluted earnings per share are as follows:

	Three Months Ended						Nine Months Ended
	September 30,						September 30,
	2012			2011			2012		2011
Numerator:
Net income (loss)	$	(7,745	)	$	(9,560	)	$	13,147	$	(29,182	)

Denominator:
Weighted average number of common shares outstanding	34,243,792			34,080,177			34,188,146		30,295,881
Effect of dilutive securities:
Stock options	—			—			82,309		—
Dilutive potential common shares	—			—			82,309		—
Shares used in calculating diluted earnings per share	34,243,792			34,080,177			34,270,455		30,295,881

The number of shares of potentially dilutive common stock related to options and warrants that were excluded from the calculation of dilutive shares since the inclusion of such shares would be anti-dilutive for the three and nine months ended September 30, 2012 and 2011, respectively, are shown below:

	Three Months Ended		Nine Months Ended
	September 30,		September 30,
	2012	2011	2012	2011
Options	5,665,046	3,830,152	5,413,073	3,830,152
Warrants	4,086	4,086	4,086	4,086
Total	5,669,132	3,834,238	5,417,159	3,834,238

STOCK-BASED COMPENSATION

9 Months Ended

Sep. 30, 2012

STOCK-BASED COMPENSATION

STOCK-BASED COMPENSATION

5. STOCK-BASED COMPENSATION

The Company recognized stock-based compensation expense, related to employee stock option awards, of $852 and $2,954 for the three and nine months ended September 30, 2012, respectively. Stock-based compensation expense, related to employee stock option awards, was $1,126 and $3,566 for the three and nine months ended September 30, 2011, respectively. At September 30, 2012, there was approximately $6,533 of pre-tax stock-based compensation expense, net of estimated forfeitures, related to unvested awards not yet recognized which is expected to be recognized over a weighted average period of 2.42 years.

A summary of option activity for the nine months ended September 30, 2012 is as follows:

	Number of		Weighted Average
	Shares		Exercise Price
Outstanding at December 31, 2011	3,858,685		$	10.36
Granted	2,493,100		2.15
Exercised	(11,436	)	1.65
Cancelled	(675,303	)	9.74
Outstanding at September 30, 2012	5,665,046		6.84

Options exercisable at September 30, 2012	2,756,107		$	10.14

Weighted average grant date fair value of options granted during the nine months ended September 30, 2012			$	1.47

For the nine months ended September 30, 2012 and 2011, the Company determined the fair value of stock options using the Black-Scholes option pricing model with the following assumptions for option grants, respectively:

	Nine Months Ended
	September 30,
	2012	2011
Expected dividend yield	—	—
Risk-free rate	0.67% - 1.15%	0.95% - 2.38%
Expected option term (in years)	5.3 – 5.5	5.5 – 5.6
Volatility	84% - 87%	77% - 80%

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

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-Name Staff Accounting Bulletin (SAB)
-Number Topic 14

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 123R
-Paragraph 64, 65, A240
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Statement of Position (SOP)
-Number 93-6
-Paragraph 53
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

RESEARCH AND DEVELOPMENT

9 Months Ended

Sep. 30, 2012

RESEARCH AND DEVELOPMENT

RESEARCH AND DEVELOPMENT

6. RESEARCH AND DEVELOPMENT

All costs associated with internal research and development as well as research and development services conducted for others are expensed as incurred. Research and development expenses include direct costs for salaries, employee benefits, subcontractors, facility related expenses, depreciation and stock-based compensation related to employees and non-employees involved in the Company’s research and development. Costs related to revenue-producing contracts and government grants are recorded as research and development expenses.

- Definition

The entire disclosure for research, development, and computer software activities, including contracts and arrangements to be performed for others and with federal government. Includes costs incurred (1) in a planned search or critical investigation aimed at discovery of new knowledge with the hope that such knowledge will be useful in developing a new product or service, a new process or technique, or in bringing about a significant improvement to an existing product or process; or (2) to translate research findings or other knowledge into a plan or design for a new product or process or for a significant improvement to an existing product or process whether intended for sale or the entity's use, during the reporting period charged to research and development projects, including the costs of developing computer software up to the point in time of achieving technological feasibility and in-process research and development acquired in a business combination consummated during the period.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 730
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6420194&loc=d3e21568-108373

Reference 2: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 730
-SubTopic 20
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-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6420387&loc=d3e23221-108380

Reference 3: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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Reference 4: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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Reference 5: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 985
-SubTopic 20
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6501960&loc=d3e128462-111756

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 86
-Paragraph 11, 12
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 2
-Paragraph 12, 13
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Audit and Accounting Guide (AAG)
-Number AAG-FGC
-Paragraph 56, 57
-IssueDate 2006-05-01
-Chapter 3
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

ADM COLLABORATION

9 Months Ended

Sep. 30, 2012

ADM COLLABORATION

ADM COLLABORATION

7. ADM COLLABORATION

In 2004, the Company signed a Technology Alliance and Option Agreement with ADM Polymer Corporation (“ADM Polymer”), a wholly-owned subsidiary of Archer Daniels Midland Company (“ADM”), to establish an alliance whereby the Company would provide technology, licenses and research and development services, and ADM Polymer would provide manufacturing services and capital necessary to produce biopolymers on a commercial scale. The Technology Alliance and Option Agreement provided ADM with an option (the “Option”) to enter into a commercial alliance for further research, development, manufacture, use, and sale of biopolymers on the terms and conditions set forth in the Commercial Alliance Agreement. In 2006, ADM exercised this Option, and the Technology Alliance and Option Agreement concluded.

The Commercial Alliance Agreement between Metabolix and ADM Polymer specified the terms and structure of the alliance. The primary function of this agreement was to establish the activities and obligations of the parties to commercialize PHA biopolymers, which have been marketed under the brand names Mirel™ and MveraTM. These activities included: the establishment of a joint venture company, Telles, LLC (“Telles”), to market and sell PHA biopolymers, the construction of a manufacturing facility capable of producing 110 million pounds of material annually (the “Commercial Manufacturing Facility”), the licensing of technology to Telles and to ADM, and the conducting of various research, development, manufacturing, sales and marketing, compounding and administrative services by the parties.

Telles was formed to: (i) serve as the commercial entity to establish and develop the commercial market for PHA biopolymers, and conduct the marketing and sales in accordance with the goals of the commercial alliance, (ii) assist in the coordination and integration of the manufacturing, compounding and marketing activities, and (iii) administer and account for financial matters on behalf of the parties. Metabolix and ADM each had a 50% ownership and voting interest in Telles.

Under the Technology Alliance and Option Agreement and Commercial Alliance Agreement, various payments were made to Metabolix by ADM as shown in the table below. All of these payments were recorded as deferred revenue on the Company’s balance sheet and were expected to be recognized on a straight line basis over a period of approximately ten years in which Metabolix would fulfill its contractual obligations during the Commercial Phase of the Commercial Alliance Agreement.

Upfront payment	$	3,000
Milestone payments	2,000
Support payments	22,050
Cost sharing payments for pre-commercial manufacturing plant construction and operations	11,835
Total	$	38,885

Under the Commercial Alliance Agreement ADM was permitted, under limited circumstances, to terminate the alliance if a change in circumstances that was not reasonably within the control of ADM made the anticipated financial return from the project inadequate or too uncertain. The agreement provided that, upon termination by ADM due to a change in circumstances, Metabolix would be permitted to continue to produce and sell PHA biopolymers, and ADM would be required to perform manufacturing services for the Company for a period of time following the termination (subject to certain payment obligations to ADM). On January 9, 2012, ADM notified the Company that it was terminating the commercial alliance effective February 8, 2012. ADM had undertaken a strategic review of its business investments and activities and made the decision to focus resources outside of Telles. As the basis for the decision, ADM indicated to the Company that the projected financial returns from the alliance were too uncertain.

The Commercial Alliance Agreement with ADM limited the rights of both ADM and the Company to work with other parties or alone in developing or commercializing certain PHAs produced through fermentation. These exclusivity obligations ended upon termination of the alliance. Also, upon termination of the alliance, Metabolix intellectual property licenses to ADM Polymer and Telles ended, with Metabolix retaining all rights to its intellectual property. ADM retained its Commercial Manufacturing Facility located in Clinton, Iowa, previously used to produce PHA biopolymers for Telles.

The Company has no further performance obligations in connection with the commercial alliance after its termination, and as a result, the entire $38,885 of deferred revenue was recognized by the Company during its fiscal quarter ended March 31, 2012.

After termination of the Commercial Alliance Agreement, the parties entered into a Settlement Agreement dated March 6, 2012 (the “Settlement Agreement”) in which the parties agreed to specific terms related to the winding up and dissolution of Telles. Under this Settlement Agreement the Company purchased certain assets of the joint venture for $2,982, including Telles’s entire inventory, exclusive and perpetual rights to all of Telles’s trademarks, and all product registrations, certifications and approvals for Telles’s PHA biopolymers. Pursuant to the Settlement Agreement, ADM relinquished any claims with respect to certain co-funded equipment previously acquired by Metabolix and situated at locations other than the Clinton, Iowa Commercial Manufacturing Facility, and Metabolix and Telles waived any rights to post-termination manufacturing and fermentation services under the Commercial Alliance Agreement. The Company assessed the market value of the various assets acquired from Telles under the Settlement Agreement and determined that the full amount of the $2,982 purchase price should be allocated to the raw material and biopolymer inventory.

Pursuant to the Settlement Agreement, Telles paid to ADM an amount equal to the aggregate cash balances of Telles totaling $3,778 on the date of the Settlement Agreement, minus $100 retained by Telles to settle any remaining trade obligations. The Company believes the remaining trade obligations of Telles at the date of execution of the Settlement Agreement did not exceed $100. In the event that ADM is required to repay to Telles or to pay to any creditor of Telles any amounts included in the $2,982 purchase price or the $3,678 distributed to ADM by Telles pursuant to the Settlement Agreement, Metabolix is obligated to reimburse ADM in an amount equal to 50% of such payments, provided that in no event would the amount to be so paid by Metabolix exceed the total of the $2,982 purchase price and the $3,678 Telles cash required to be so repaid or reimbursed by ADM. The Company is not aware of any such third party creditor claims, and believes that the likelihood that it will be required to reimburse ADM under this provision is remote and therefore no liability for this potential obligation is included in the Company’s balance sheet at September 30, 2012.

INCOME TAXES

9 Months Ended

Sep. 30, 2012

INCOME TAXES

INCOME TAXES

8. INCOME TAXES

The Company follows the accounting guidance related to income taxes including guidance which addresses accounting for uncertainty in income taxes. This guidance prescribes a threshold for the financial statement recognition and measurement of a tax position taken or expected to be taken in a tax return. It also provides guidance on derecognition, classification, interest and penalties, accounting in interim periods, disclosures and transitions. The Company had no amounts recorded for any unrecognized tax benefits as of September 30, 2012 or December 31, 2011.

The tax years 2009 through 2011 remain open to examination by major taxing jurisdictions to which the Company is subject, which are primarily in the U.S. Additionally, the Company can be audited for any loss year up to three years after the year in which the loss is utilized to offset taxable income. This would include loss years prior to 2009.

The Company’s policy is to record estimated interest and penalties related to uncertain tax positions in income tax expense. As of September 30, 2012 and December 31, 2011, the Company had no accrued interest or penalties recorded related to uncertain tax positions.

At December 31, 2011, the Company had net operating loss (NOL) carryforwards for federal and state income tax purposes of $180,436 and $142,414, respectively. Included in the federal and state NOL carryforwards is approximately $19,201 of deductions related to the exercise of stock options subsequent to the adoption of amended accounting guidance related to stock-based compensation. This amount represents an excess tax benefit as defined under the amended accounting guidance related to stock-based compensation and has not been recorded as a deferred tax asset. The Company’s existing federal and state NOL carryforwards begin to expire in 2012. The Company also had available research and development credits for federal and state income tax purposes of approximately $4,502 and $3,200, respectively. The federal and state research and development credits will begin to expire in 2014 and 2016 respectively. As of December 31, 2011 the Company also had available investment tax credits for state income tax purposes of $117 which also began to expire in 2012. Management of the Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets, which are comprised principally of NOL carryforwards and research and development credits. Under the applicable accounting standards, management has considered the Company’s history of losses and concluded that it is more likely than not that the Company will not recognize the benefits of federal and state deferred tax assets. Accordingly, a full valuation allowance has been established against the deferred tax assets.

Utilization of the NOL and research and development credit carryforwards may be subject to a substantial annual limitation under Section 382 of the Internal Revenue Code of 1986 due to ownership change limitations that have occurred previously or that could occur in the future. These ownership changes may limit the amount of NOL and research and development credit carryforwards that can be utilized annually to offset future taxable income and tax, respectively. The Company has completed an evaluation of ownership changes through December 31, 2011 to assess whether utilization of the Company’s NOL or research and development credit carryforwards would be subject to an annual limitation under Section 382, and has determined that its NOL and research and development credit carryforwards are not subject to limitation. To the extent an ownership change occurs in the future, the NOL and credit carryforwards may be subject to limitation.

- Definition

The entire disclosure for income taxes. Disclosures may include net deferred tax liability or asset recognized in an enterprise's statement of financial position, net change during the year in the total valuation allowance, approximate tax effect of each type of temporary difference and carryforward that gives rise to a significant portion of deferred tax liabilities and deferred tax assets, utilization of a tax carryback, and tax uncertainties information.

+ References

+ Details

INVESTMENTS

9 Months Ended

Sep. 30, 2012

Investments

Investments

9. INVESTMENTS

Investments consist of the following:

	Amortized		Unrealized					Market
	Cost		Gain		(Loss)			Value
September 30, 2012
Short-term investments
Corporate Debt	$	6,952	$	1	$	(1	)	$	6,952
Government-sponsored enterprises	23,462		5		(1		)	23,466
Long-term investments
Government-sponsored enterprises	5,761		6		—			5,767
Total	$	36,175	$	12	$	(2	)	$	36,185

December 31, 2011
Short-term investments
Corporate Debt	$	29,854	$	13	$	(1	)	$	29,866
Government-sponsored enterprises	25,709		5		(2		)	25,712
Long-term investments
Government-sponsored enterprises	1,503		—		—			1,503
Total	$	57,066	$	18	$	(3	)	$	57,081

Long-term investments have maturity dates of two years or less.

- Definition

The entire disclosure for investments in certain debt and equity securities.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-Glossary Debt Security
-URI http://asc.fasb.org/extlink&oid=6509901

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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Reference 3: http://www.xbrl.org/2003/role/presentationRef
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Reference 4: http://www.xbrl.org/2003/role/presentationRef
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Reference 5: http://www.xbrl.org/2003/role/presentationRef
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Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

ACCRUED EXPENSES

9 Months Ended

Sep. 30, 2012

ACCRUED EXPENSES

ACCRUED EXPENSES

10. ACCRUED EXPENSES

Accrued expenses consisted of the following at:

	September 30, 2012		December 31, 2011
Employee compensation and benefits	$	2,141	$	1,740
Professional services	200		185
Intellectual property	150		240
Other	997		1,409
Total accrued expenses	$	3,488	$	3,574

SEGMENT INFORMATION

9 Months Ended

Sep. 30, 2012

SEGMENT INFORMATION

SEGMENT INFORMATION

11. SEGMENT INFORMATION

The accounting guidance for segment reporting establishes standards for reporting information on operating segments in annual financial statements. The Company operates in one segment, which is the business of developing and commercializing technologies for the production of polymers and chemicals in plants and in microbes. The Company’s chief operating decision-maker does not manage any part of the Company separately, and the allocation of resources and assessment of performance are based on the Company’s consolidated operating results. As of September 30, 2012, less than 10% of the Company’s combined total assets were located outside of the United States and the reported net income outside of the United States for the three and nine months ended September 30, 2012 was less than 10% of the combined net income of the consolidated Company.

- Definition

The entire disclosure for reporting segments including data and tables. Reportable segments include those that meet any of the following quantitative thresholds a) it's reported revenue, including sales to external customers and intersegment sales or transfers is 10 percent or more of the combined revenue, internal and external, of all operating segments b) the absolute amount of its reported profit or loss is 10 percent or more of the greater, in absolute amount of 1) the combined reported profit of all operating segments that did not report a loss or 2) the combined reported loss of all operating segments that did report a loss c) its assets are 10 percent or more of the combined assets of all operating segments.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 280
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-URI http://asc.fasb.org/extlink&oid=6534315&loc=d3e8981-108599

Reference 2: http://www.xbrl.org/2003/role/presentationRef
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-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

COMMITMENTS AND CONTINGENCIES

9 Months Ended

Sep. 30, 2012

COMMITMENTS AND CONTINGENCIES.

COMMITMENTS AND CONTINGENCIES

12. COMMITMENTS AND CONTINGENCIES

Legal Proceedings

On February 17, 2012, a purported shareholder class action, Hilary Coyne v. Metabolix, Inc., Richard P. Eno, and Joseph Hill, Civil Action 1:12-cv-10318 (the “class action”), was filed in the United States District Court for the District of Massachusetts, naming the Company and certain officers of the Company as defendants. The class action alleges that the Company made material misrepresentations and/or omissions of material fact in the Company’s disclosures during the period from March 10, 2010 through its January 12, 2012 press release announcing that ADM had given notice of termination of the Telles joint venture for PHA biopolymers, all in violation of Sections 10(b) and 20(a) of the Securities Exchange Act and Rule 10b-5. The class action seeks certification as a class action, compensatory damages in an unspecified amount, plaintiff’s costs and attorneys’ fees, and unspecified equitable or injunctive relief. The plaintiff filed an amended complaint on October 15, 2012 that supersedes the initial complaint and demands identical relief based on substantially similar allegations.

On March 7, 2012, a purported derivative lawsuit, Childs v. Kouba et al., Civil Action 12-0892 (the “derivative action”), was filed in Massachusetts Superior Court for Middlesex County, on behalf of the Company against members of the Company’s Board of Directors for alleged breaches of their fiduciary duties and based on a nearly identical set of alleged facts as those asserted in the class action. The derivative action seeks compensatory damages in an unspecified amount, plaintiff’s costs and attorneys’ fees, and unspecified equitable or injunctive relief. The parties in the derivative action filed and the court granted a joint motion to stay the derivative action until after resolution of the anticipated motion to dismiss in the class action.

We are currently unable to assess the probability of loss or estimate a range of potential loss, if any, associated with these matters because they are at an early stage.

- Definition

The entire disclosure for commitments and contingencies.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
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Reference 7: http://www.xbrl.org/2003/role/presentationRef
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

FAIR VALUE MEASUREMENTS

9 Months Ended

Sep. 30, 2012

FAIR VALUE MEASUREMENTS

FAIR VALUE MEASUREMENTS

13. FAIR VALUE MEASUREMENTS

The Company has certain financial assets recorded at fair value which have been classified as either Level 1 or 2 within the fair value hierarchy as described in the accounting standards for fair value measurements. Fair values determined by Level 1 inputs utilize observable data such as quoted prices in active markets. Fair values determined by Level 2 inputs utilize data points other than quoted prices in active markets that are observable either directly or indirectly. Fair values determined by Level 3 inputs utilize unobservable data points in which there is little or no market data, which require the reporting entity to develop its own assumptions. At September 30, 2012 and December 31, 2011, the Company did not own any Level 3 financial assets.

The Company’s financial assets classified as Level 2 have been initially valued at the transaction price and subsequently valued typically utilizing third party pricing services. Because the Company’s investment portfolio may include securities that do not always trade on a daily basis, the pricing services use many observable market inputs to determine value including reportable trades, benchmark yields and benchmarking of like securities. The Company validates the prices provided by the third party pricing services by reviewing their pricing methods and obtaining market values from other pricing sources. After completing the validation procedures, the Company did not adjust or override any fair value measurements provided by these pricing services as of September 30, 2012 or December 31, 2011.

The tables below present information about the Company’s assets that are measured at fair value on a recurring basis as of September 30, 2012 and December 31, 2011 and indicate the fair value hierarchy of the valuation techniques utilized to determine such fair value.

	Fair value measurements at reporting date using
	Quoted prices in active
	markets for identical		Significant other		Significant
	assets		observable inputs		unobservable inputs		Balance as of
Description	(Level 1)		(Level 2)		(Level 3)		September 30, 2012
Cash equivalents:
Corporate debt	$	—	$	—	$	—	$	—
Government securities	—		—		—		—
Money market funds	12,686		—		—		12,686
Short-term investments:
Corporate debt	—		6,952		—		6,952
Government securities	—		23,466		—		23,466
Long-term investments:
Government securities	—		5,767		—		5,767
	$	12,686	$	36,185	$	—	$	48,871

	Fair value measurements at reporting date using
Description	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Balance as of December 31, 2011
Cash equivalents:
Money market funds	$	18,262	$	—	$	—	$	18,262
Short-term investments:
Corporate debt	—		29,866		—		29,866
Government securities	—		25,712		—		25,712
Long-term investments:
Government securities	—		1,503		—		1,503
Total	$	18,262	$	57,081	$	—	$	75,343

In the tables above as of September 30, 2012 and December 31, 2011, all corporate debt securities were issued by financial institutions under the Temporary Liquidity Guarantee Program.

The Company considers all highly liquid investments purchased with an original maturity date of ninety days or less at the date of purchase to be cash equivalents, and investments purchased with an original maturity date of ninety days or more at the date of purchase and a maturity date of one year or less at the balance sheet date to be short-term investments. All other investments are classified as long-term.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References

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-Name Accounting Standards Codification
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-Number 107
-Paragraph 15B
-Subparagraph a, b
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Reference 8: http://www.xbrl.org/2003/role/presentationRef
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Reference 9: http://www.xbrl.org/2003/role/presentationRef
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Reference 12: http://www.xbrl.org/2003/role/presentationRef
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Reference 13: http://www.xbrl.org/2003/role/presentationRef
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-Number 107
-Paragraph 3, 10, 14, 15
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

RELATED PARTIES

9 Months Ended

Sep. 30, 2012

RELATED PARTIES

RELATED PARTIES

14. RELATED PARTIES

The Company engaged in various transactions with Tepha, Inc., a related party, and recorded $28 and $122 of license and royalty revenue during the three months and nine months ended September 30, 2012, respectively. During the three and nine months ended September 30, 2011, the Company recorded license and royalty revenue from Tepha, Inc. of $26 and $419, respectively. As of September 30, 2012 and December 31, 2011, the Company had no outstanding receivables due from Tepha.

The Company had various transactions with its former alliance partner ADM, a related party, during the nine months ended September 30, 2012 and 2011. The Company had an outstanding receivable balance of $203 due from ADM at December 31, 2011 that has subsequently been collected. No receivables remain outstanding with ADM at September 30, 2012.

The Company also had various transactions with Telles. As of September 30, 2012, the Company had no remaining outstanding receivable due from Telles. The Company collected its fully reserved $51 receivable from Telles during the three months ended September 30, 2012. The Company had an outstanding receivable balance of $108 due from Telles as of December 31, 2011. For more information on the Company’s related party transactions, please see Note 8 to the Company’s audited financial statements included in its Annual Report on Form 10-K for the year ended December 31, 2011.

- Definition

The entire disclosure for related party transactions. Examples of related party transactions include transactions between (a) a parent company and its subsidiary; (b) subsidiaries of a common parent; (c) and entity and its principal owners; and (d) affiliates.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
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+ Details

COMMON STOCK

9 Months Ended

Sep. 30, 2012

COMMON STOCK

COMMON STOCK

15. COMMON STOCK

Common Stock Issuances

During May 2011, the Company completed a public offering of 7,130,000 shares of its common stock at a price of $7.25 per share. Net proceeds were $49,333 after deducting underwriting discounts, commissions and offering costs of $2,360. The Company is using the proceeds from the offering for working capital and other general corporate purposes.

- Definition

The entire disclosure for shareholders' equity, comprised of portions attributable to the parent entity and noncontrolling interest, if any, including other comprehensive income (as applicable). Including, but not limited to: (1) balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings; (2) accumulated balance for each classification of other comprehensive income and total amount of comprehensive income; (3) amount and nature of changes in separate accounts, including the number of shares authorized and outstanding, number of shares issued upon exercise and conversion, and for other comprehensive income, the adjustments for reclassifications to net income; (4) rights and privileges of each class of stock authorized; (5) basis of treasury stock, if other than cost, and amounts paid and accounting treatment for treasury stock purchased significantly in excess of market; (6) dividends paid or payable per share and in the aggregate for each class of stock for each period presented; (7) dividend restrictions and accumulated preferred dividends in arrears (in aggregate and per share amount); (8) retained earnings appropriations or restrictions, such as dividend restrictions; (9) impact of change in accounting principle, initial adoption of new accounting principle and correction of an error in previously issued financial statements; (10) shares held in trust for Employee Stock Ownership Plan (ESOP); (11) deferred compensation related to issuance of capital stock; (12) note received for issuance of stock; (13) unamortized discount on shares; (14) description, terms, and number of warrants or rights outstanding; (15) shares under subscription and subscription receivables, effective date of new retained earnings after quasi-reorganization and deficit eliminated by quasi-reorganization and, for a period of at least ten years after the effective date, the point in time from which the new retained dates; and (16) retroactive effective of subsequent change in capital structure.

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+ Details

INVENTORY

9 Months Ended

Sep. 30, 2012

INVENTORY

INVENTORY

16. INVENTORY

During the quarter ended March 31, 2012, the Company acquired raw material and finished goods inventory of biopolymer from Telles, as a result of the termination of the joint venture with ADM. As of September 30, 2012, inventory consisted of the following:

	September 30, 2012
Raw materials	$	806
Work-in-process	8
Finished goods	2,214
Total inventory	$	3,028

The Company did not own inventory at December 31, 2011.

RESTRUCTURING

9 Months Ended

Sep. 30, 2012

RESTRUCTURING

RESTRUCTURING

17. RESTRUCTURING

In connection with the Telles termination, in the first quarter of 2012, the Company restructured its biopolymers business and downsized its operations to more appropriately align its 2012 business priorities and strategic plans with current cash and investment resources. The Company has recognized $920 of restructuring charges through the nine months ended September 30, 2012, as follows:

	Original Charges and Amounts Accrued		(Reversals) or Adjustments to Charges		Amounts Paid through September 30, 2012		Amounts Accrued at September 30, 2012
Employee severance, benefits and related costs	$	837	$	18	$	855	$	—
Contract termination costs	22		43		65		—
	$	859	$	61	$	920	$	—

In September 2012, the Company terminated the lease for its former corporate office located at One Kendall Square, Cambridge, Massachusetts, paying an early termination fee of $43. The lease had been contracted to end in May 2014.

- Definition

The entire disclosure for restructuring and related activities. Description of restructuring activities such as exit and disposal activities, include facts and circumstances leading to the plan, the expected plan completion date, the major types of costs associated with the plan activities, total expected costs, the accrual balance at the end of the period, and the periods over which the remaining accrual will be settled.

+ References + Details

ACCOUNTING POLICIES (Policies)

9 Months Ended

Sep. 30, 2012

ACCOUNTING POLICIES

Disclosure of accounting policy for major classes of inventories, bases of stating inventories (for example, lower of cost or market), methods by which amounts are added and removed from inventory classes (for example, FIFO, LIFO, or average cost), loss recognition on impairment of inventories, and situations in which inventories are stated above cost. If inventory is carried at cost, this disclosure includes the nature of the cost elements included in inventory.

+ References

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-Article 5

+ Details

- Definition

Disclosure of accounting policy for revenue recognition. If the entity has different policies for different types of revenue transactions, the policy for each material type of transaction is generally disclosed. If a sales transaction has multiple element arrangements (for example, delivery of multiple products, services or the rights to use assets) the disclosure may indicate the accounting policy for each unit of accounting as well as how units of accounting are determined and valued. The disclosure may encompass important judgment as to appropriateness of principles related to recognition of revenue. The disclosure also may indicate the entity's treatment of any unearned or deferred revenue that arises from the transaction.

+ References + Details

BASIC AND DILUTED NET INCOME (LOSS) PER SHARE (Tables)

9 Months Ended

Sep. 30, 2012

BASIC AND DILUTED NET INCOME (LOSS) PER SHARE

Schedule of shares used to calculate diluted earnings per share

	Three Months Ended						Nine Months Ended
	September 30,						September 30,
	2012			2011			2012		2011
Numerator:
Net income (loss)	$	(7,745	)	$	(9,560	)	$	13,147	$	(29,182	)

Denominator:
Weighted average number of common shares outstanding	34,243,792			34,080,177			34,188,146		30,295,881
Effect of dilutive securities:
Stock options	—			—			82,309		—
Dilutive potential common shares	—			—			82,309		—
Shares used in calculating diluted earnings per share	34,243,792			34,080,177			34,270,455		30,295,881

Schedule of number of shares of potentially dilutive common stock related to options and warrants that were excluded

	Three Months Ended		Nine Months Ended
	September 30,		September 30,
	2012	2011	2012	2011
Options	5,665,046	3,830,152	5,413,073	3,830,152
Warrants	4,086	4,086	4,086	4,086
Total	5,669,132	3,834,238	5,417,159	3,834,238

STOCK-BASED COMPENSATION (Tables)

9 Months Ended

Sep. 30, 2012

STOCK-BASED COMPENSATION

Summary of option activity

	Number of		Weighted Average
	Shares		Exercise Price
Outstanding at December 31, 2011	3,858,685		$	10.36
Granted	2,493,100		2.15
Exercised	(11,436	)	1.65
Cancelled	(675,303	)	9.74
Outstanding at September 30, 2012	5,665,046		6.84

Options exercisable at September 30, 2012	2,756,107		$	10.14

Weighted average grant date fair value of options granted during the nine months ended September 30, 2012			$	1.47

Schedule of assumptions used in determining fair value of stock options

	Nine Months Ended
	September 30,
	2012	2011
Expected dividend yield	—	—
Risk-free rate	0.67% - 1.15%	0.95% - 2.38%
Expected option term (in years)	5.3 – 5.5	5.5 – 5.6
Volatility	84% - 87%	77% - 80%

ADM COLLABORATION (Tables)

9 Months Ended

Sep. 30, 2012

ADM COLLABORATION

Schedule of payments received that were recorded as deferred revenue under the Technology Alliance and Option Agreement and Commercial Alliance Agreement

Upfront payment	$	3,000
Milestone payments	2,000
Support payments	22,050
Cost sharing payments for pre-commercial manufacturing plant construction and operations	11,835
Total	$	38,885

INVESTMENTS (Tables)

9 Months Ended

Sep. 30, 2012

Investments

Schedule of investments

	Amortized		Unrealized					Market
	Cost		Gain		(Loss)			Value
September 30, 2012
Short-term investments
Corporate Debt	$	6,952	$	1	$	(1	)	$	6,952
Government-sponsored enterprises	23,462		5		(1		)	23,466
Long-term investments
Government-sponsored enterprises	5,761		6		—			5,767
Total	$	36,175	$	12	$	(2	)	$	36,185

December 31, 2011
Short-term investments
Corporate Debt	$	29,854	$	13	$	(1	)	$	29,866
Government-sponsored enterprises	25,709		5		(2		)	25,712
Long-term investments
Government-sponsored enterprises	1,503		—		—			1,503
Total	$	57,066	$	18	$	(3	)	$	57,081

ACCRUED EXPENSES (Tables)

9 Months Ended

Sep. 30, 2012

ACCRUED EXPENSES

Schedule of accrued expenses

	September 30, 2012		December 31, 2011
Employee compensation and benefits	$	2,141	$	1,740
Professional services	200		185
Intellectual property	150		240
Other	997		1,409
Total accrued expenses	$	3,488	$	3,574

FAIR VALUE MEASUREMENTS (Tables)

9 Months Ended

Sep. 30, 2012

FAIR VALUE MEASUREMENTS

Schedule of information about assets that are measured at fair value on a recurring basis

	Fair value measurements at reporting date using
	Quoted prices in active
	markets for identical		Significant other		Significant
	assets		observable inputs		unobservable inputs		Balance as of
Description	(Level 1)		(Level 2)		(Level 3)		September 30, 2012
Cash equivalents:
Corporate debt	$	—	$	—	$	—	$	—
Government securities	—		—		—		—
Money market funds	12,686		—		—		12,686
Short-term investments:
Corporate debt	—		6,952		—		6,952
Government securities	—		23,466		—		23,466
Long-term investments:
Government securities	—		5,767		—		5,767
	$	12,686	$	36,185	$	—	$	48,871

	Fair value measurements at reporting date using
Description	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Balance as of December 31, 2011
Cash equivalents:
Money market funds	$	18,262	$	—	$	—	$	18,262
Short-term investments:
Corporate debt	—		29,866		—		29,866
Government securities	—		25,712		—		25,712
Long-term investments:
Government securities	—		1,503		—		1,503
Total	$	18,262	$	57,081	$	—	$	75,343

- Definition

Tabular disclosure of assets, including [financial] instruments measured at fair value that are classified in stockholders' equity, if any, by class that are measured at fair value on a recurring basis. The disclosures contemplated herein include the fair value measurements at the reporting date by the level within the fair value hierarchy in which the fair value measurements in their entirety fall, segregating fair value measurements using quoted prices in active markets for identical assets (Level 1), significant other observable inputs (Level 2), and significant unobservable inputs (Level 3).

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INVENTORY (Tables)

9 Months Ended

Sep. 30, 2012

INVENTORY

Schedule of inventory

	September 30, 2012
Raw materials	$	806
Work-in-process	8
Finished goods	2,214
Total inventory	$	3,028

RESTRUCTURING (Tables)

9 Months Ended

Sep. 30, 2012

RESTRUCTURING

Schedule of accrued restructuring charges

	Original Charges and Amounts Accrued		(Reversals) or Adjustments to Charges		Amounts Paid through September 30, 2012		Amounts Accrued at September 30, 2012
Employee severance, benefits and related costs	$	837	$	18	$	855	$	—
Contract termination costs	22		43		65		—
	$	859	$	61	$	920	$	—

ACCOUNTING POLICIES (Details)	9 Months Ended
ACCOUNTING POLICIES (Details)	Sep. 30, 2012
ACCOUNTING POLICIES
Period for which company is having option of accepting returns from customers	60 days

BASIC AND DILUTED NET INCOME (LOSS) PER SHARE (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Numerator:
Net income (loss)	$ (7,745)	$ (9,560)	$ 13,147	$ (29,182)
Denominator:
Weighted average number of common shares outstanding	34,243,792	34,080,177	34,188,146	30,295,881
Effect of dilutive securities:
Stock options (in shares)			82,309
Dilutive potential common shares			82,309
Shares used in calculating diluted earnings per share	34,243,792	34,080,177	34,270,455	30,295,881
Antidilutive securities
Antidilutive common stock excluded from the calculation of dilutive shares	5,669,132	3,834,238	5,417,159	3,834,238
Options
Antidilutive securities
Antidilutive common stock excluded from the calculation of dilutive shares	5,665,046	3,830,152	5,413,073	3,803,152
Warrants
Antidilutive securities
Antidilutive common stock excluded from the calculation of dilutive shares	4,086	4,086	4,086	4,086

STOCK-BASED COMPENSATION (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011
Stock-based compensation
Stock-based compensation expense related to employee stock option awards	$ 852	$ 1,126	$ 2,954	$ 3,566
Stock-based compensation expense, net of estimated forfeitures, related to unvested awards not yet recognized	$ 6,533		$ 6,533
Weighted average period over which unrecognized compensation expense is expected to be recognized			2 years 5 months 1 day
Number of Shares
Outstanding at the beginning of the period (in shares)			3,858,685
Granted (in shares)			2,493,100
Exercised (in shares)			(11,436)
Cancelled (in shares)			(675,303)
Outstanding at the end of the period (in shares)	5,665,046		5,665,046
Options exercisable at the end of the period (in shares)	2,756,107		2,756,107
Weighted Average Exercise Price
Outstanding at the beginning of the period (in dollars per share)			$ 10.36
Granted (in dollars per share)			2.15
Exercised (in dollars per share)			1.65
Cancelled (in dollars per share)			9.74
Outstanding at the end of the period (in dollars per share)	$ 6.84		6.84
Options exercisable at the end of the period (in dollars per share)	$ 10.14		10.14
Weighted average grant date fair value of options granted (in dollars per share)			$ 1.47
Assumptions used to determine fair value of stock options
Risk-free rate, minimum (as a percent)			0.67%	0.95%
Risk-free rate, maximum (as a percent)			1.15%	2.38%
Volatility, minimum (as a percent)			84.00%	77.00%
Volatility, maximum (as a percent)			87.00%	80.00%
Minimum
Assumptions used to determine fair value of stock options
Expected option term			5 years 3 months 18 days	5 years 6 months
Maximum
Assumptions used to determine fair value of stock options
Expected option term			5 years 6 months	5 years 7 months 6 days

ADM COLLABORATION (Details) $ in Thousands, pound in Millions	1 Months Ended		3 Months Ended	7 Months Ended	9 Months Ended	12 Months Ended
	Mar. 31, 2012 USD ($)	Feb. 29, 2012	Mar. 31, 2012 USD ($)	Sep. 30, 2012 USD ($)	Sep. 30, 2012 USD ($)	Dec. 31, 2006 pound	Mar. 06, 2012 USD ($)	Feb. 08, 2012 USD ($)	Dec. 31, 2011 USD ($)	Sep. 30, 2011 USD ($)	Dec. 31, 2010 USD ($)
Significant collaboration
Deferred revenue recognized					$ 38,885
Aggregate cash balances of joint venture				$ 17,405	$ 17,405				$ 21,277	$ 17,392	$ 12,526
Commercial Alliance Agreement
Significant collaboration
Period over which payments recorded as deferred revenue is expected to be recognized		10 years
Commercial Alliance Agreement \| Telles
Significant collaboration
Ownership and voting interest in Telles (as a percent)						50.00%
Purchase price to acquire assets of joint venture	$ 2,982
Aggregate cash balances of joint venture							$ 3,778
Amount retained by joint venture to settle any remaining trade obligations							100
Commercial Alliance Agreement \| Telles \| Maximum
Significant collaboration
Remaining trade obligations of joint venture							$ 100
Commercial Alliance Agreement \| ADM Polymer
Significant collaboration
Annual production capability of manufacturing facility that will be constructed under the agreement (in pounds) \| pound						110
Total deferred revenue								$ 38,885
Deferred revenue recognized			$ 38,885
Percentage of reimbursement by the entity to ADM for third party claims of Telles to the extent of assets distributed				50.00%	50.00%
Commercial Alliance Agreement \| ADM Polymer \| Upfront payment
Significant collaboration
Total deferred revenue								3,000
Commercial Alliance Agreement \| ADM Polymer \| Milestone payments
Significant collaboration
Total deferred revenue								2,000
Commercial Alliance Agreement \| ADM Polymer \| Support payments
Significant collaboration
Total deferred revenue								22,050
Commercial Alliance Agreement \| ADM Polymer \| Cost sharing payments for pre-commercial manufacturing plant construction and operations
Significant collaboration
Total deferred revenue								$ 11,835
Commercial Alliance Agreement \| ADM Polymer \| Telles
Significant collaboration
Ownership and voting interest in Telles (as a percent)						50.00%
Cash distributed by joint venture				$ 3,678

INCOME TAXES (Details) - USD ($) $ in Thousands	9 Months Ended
INCOME TAXES (Details) - USD ($) $ in Thousands	Sep. 30, 2012	Dec. 31, 2011
INCOME TAXES
Maximum period to audit for loss	3 years
Net operating loss carryforwards
Deduction related to the exercise of stock options		$ 19,201
Federal
Net operating loss carryforwards
NOL carryforwards		180,436
State
Net operating loss carryforwards
NOL carryforwards		$ 142,414

INCOME TAXES (Details 2) $ in Thousands	Dec. 31, 2011 USD ($)
Federal \| Research and development
Tax credits
Available tax credits	$ 4,502
State \| Research and development
Tax credits
Available tax credits	3,200
State \| Investment
Tax credits
Available tax credits	$ 117

INVESTMENTS (Details) - USD ($) $ in Thousands	9 Months Ended	12 Months Ended
INVESTMENTS (Details) - USD ($) $ in Thousands	Sep. 30, 2012	Dec. 31, 2011
Investments
Amortized Cost	$ 36,175	$ 57,066
Unrealized Gain	12	18
Unrealized (Loss)	(2)	(3)
Market Value	$ 36,185	57,081
Maximum maturity period of long-term investments	2 years
Short-term investments \| Corporate debt
Investments
Amortized Cost	$ 6,952	29,854
Unrealized Gain	1	13
Unrealized (Loss)	(1)	(1)
Market Value	6,952	29,866
Short-term investments \| Government-sponsored enterprises
Investments
Amortized Cost	23,462	25,709
Unrealized Gain	5	5
Unrealized (Loss)	(1)	(2)
Market Value	23,466	25,712
Long-term investments \| Government-sponsored enterprises
Investments
Amortized Cost	5,761	1,503
Unrealized Gain	6
Market Value	$ 5,767	$ 1,503

ACCRUED EXPENSES (Details) - USD ($) $ in Thousands	Sep. 30, 2012	Dec. 31, 2011
ACCRUED EXPENSES
Employee compensation and benefits	$ 2,141	$ 1,740
Professional services	200	185
Intellectual property	150	240
Other	997	1,409
Total accrued expenses	$ 3,488	$ 3,574

- Definition

Carrying value as of the balance sheet date of obligations incurred through that date and payable for professional fees, such as for legal and accounting services received. Used to reflect the current portion of the liabilities (due within one year or within the normal operating cycle if longer).

+ References + Details

- Definition

Carrying value as of the balance sheet date of obligations incurred through that date and payable arising from transactions not otherwise specified in the taxonomy. Used to reflect the current portion of the liabilities (due within one year or within the normal operating cycle if longer).

+ References + Details

SEGMENT INFORMATION (Details)	9 Months Ended
SEGMENT INFORMATION (Details)	Sep. 30, 2012 segment
SEGMENT INFORMATION
Number of operating segments	1

FAIR VALUE MEASUREMENTS (Details) - USD ($) $ in Thousands	Sep. 30, 2012	Dec. 31, 2011
Fair value measurements
Short-term investments	$ 30,418	$ 55,578
Long-term investments	5,767	1,503
Recurring \| Quoted prices in active markets for identical assets (Level 1)
Fair value measurements
Total	12,686	18,262
Recurring \| Quoted prices in active markets for identical assets (Level 1) \| Money Market funds
Fair value measurements
Cash equivalents:	12,686	18,262
Recurring \| Significant other observable inputs (Level 2)
Fair value measurements
Total	36,185	57,081
Recurring \| Significant other observable inputs (Level 2) \| Corporate debt
Fair value measurements
Short-term investments	6,952	29,866
Recurring \| Significant other observable inputs (Level 2) \| Government securities
Fair value measurements
Short-term investments	23,466	25,712
Long-term investments	5,767	1,503
Recurring \| Balance as of the end of the period
Fair value measurements
Total	48,871	75,343
Recurring \| Balance as of the end of the period \| Money Market funds
Fair value measurements
Cash equivalents:	12,686	18,262
Recurring \| Balance as of the end of the period \| Corporate debt
Fair value measurements
Short-term investments	6,952	29,866
Recurring \| Balance as of the end of the period \| Government securities
Fair value measurements
Short-term investments	23,466	25,712
Long-term investments	$ 5,767	$ 1,503

RELATED PARTIES (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
RELATED PARTIES (Details) - USD ($) $ in Thousands	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011	Dec. 31, 2011
Related parties
License and royalty revenue	$ 28	$ 26	$ 162	$ 419
Outstanding receivable					$ 311
Tepha, Inc.
Related parties
License and royalty revenue	28	$ 26	$ 122	$ 419
ADM Polymer
Related parties
Outstanding receivable					203
Telles
Related parties
Collection of fully reserved receivable	$ 51
Outstanding receivable					$ 108

- Definition

The aggregate amount of receivables to be collected from related parties where one party can exercise control or significant influence over another party; including affiliates, owners or officers and their immediate families, pension trusts, and so forth, at the financial statement date. which are usually due within one year (or one business cycle).

+ References + Details

- Definition

Amount of revenue, fees and commissions earned from transactions between (a) a parent company and its subsidiaries; (b) subsidiaries of a common parent; (c) an entity and trusts for the benefit of employees, for example, but not limited to, pension and profit-sharing trusts that are managed by or under the trusteeship of the entity's management; (d) an entity and its principal, owners, management, or members of their immediate families; and (e) affiliates.

+ References + Details

COMMON STOCK (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	9 Months Ended
	May 31, 2011	Sep. 30, 2011
COMMON STOCK
Number of shares of common stock issued in public offering	7,130,000
Issuance price per share (in dollars per share)	$ 7.25
Net proceeds from public offering	$ 49,333	$ 49,333
Underwriting discounts, commissions and offering costs	$ 2,360

INVENTORY (Details) $ in Thousands	Sep. 30, 2012 USD ($)
INVENTORY
Raw materials	$ 806
Work-in-process	8
Finished goods	2,214
Total inventory	$ 3,028

RESTRUCTURING (Details) $ in Thousands	9 Months Ended
RESTRUCTURING (Details) $ in Thousands	Sep. 30, 2012 USD ($)
RESTRUCTURING
Restructuring charges recognized	$ 920
Changes in restructuring charges
Amounts accrued at the beginning of the period	859
(Reversals) or Adjustments to Charges	61
Amounts Paid	920
Employee severance, benefits and related costs
Changes in restructuring charges
Amounts accrued at the beginning of the period	837
(Reversals) or Adjustments to Charges	18
Amounts Paid	855
Contract termination costs
Changes in restructuring charges
Amounts accrued at the beginning of the period	22
(Reversals) or Adjustments to Charges	43
Amounts Paid	$ 65

- Definition

Amount of any reversal and other adjustment made during the period to the amount of a previously accrued liability for a specified type of restructuring cost, excluding adjustments for costs incurred during the period, costs settled during the period, and foreign currency translation adjustments.

+ References + Details